Day 3: Engage!
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Pjotr Prins
Apr 7, 2020, 11:01:52 AM4/7/20
to virtual biohackathon COVID-19 2020
Dear all,
We have over 500 people watching Slack and there is a lot of activity in
several channels. This is just great!
Even so, not everyone is participating actively, and I would like to give a
shout out to everyone who would like to contribute something but has no idea
how to start. There are several options:
1. Engage with an existing channel. When you see people working on a topic fork
the code or docs and try to contribute something. Accepted work gets your
name up there with the others.
2. If you have your own project announce it on a channel and work on that. Make
it part of the group reporting efforts.
There are many experienced people here and no one minds an offer of help! A
biohackathon is also meant to make new friends and find people who work on
topics of your interest. Use this window of opportunity! Don't be shy, in other
words!
We have over 500 people watching Slack and there is a lot of activity in
several channels. This is just great!
Even so, not everyone is participating actively, and I would like to give a
shout out to everyone who would like to contribute something but has no idea
how to start. There are several options:
1. Engage with an existing channel. When you see people working on a topic fork
the code or docs and try to contribute something. Accepted work gets your
name up there with the others.
2. If you have your own project announce it on a channel and work on that. Make
it part of the group reporting efforts.
There are many experienced people here and no one minds an offer of help! A
biohackathon is also meant to make new friends and find people who work on
topics of your interest. Use this window of opportunity! Don't be shy, in other
words!
Pjotr Prins
Apr 7, 2020, 11:48:21 AM4/7/20
to virtual biohackathon COVID-19 2020
# Day 3: Start reporting
Tomorrow we have the midterm webinar. All groups will be asked to
update their slides.
Every group should also think about their mini-publication! Remember
a mini-publication consists of the following sections
1. Description of problem
2. Description of state-of-the-art
3. Results of work during BioHackathon
4. Future work
This can simply be done in a Markdown document hosted on git. An example
can be found here
https://raw.githubusercontent.com/biohackrxiv/bhxiv-gen-pdf/master/example/logic/paper.md
which will be converted into a PDF that looks like
https://github.com/biohackrxiv/bhxiv-gen-pdf/blob/master/example/logic/LogicProgramming.pdf
These PDFs will be published with a DOI on
https://biohackrxiv.org/. If you are interested: during the
BioHackathon we are working on guidelines which can be found in the
BioHackrXiv channel on Slack.
We suggest to start reporting *today* by simply listing your
achievements and repositories in a Markdown document. You can add a
URL to that report on the group wiki today. If we find nothing we'll
approach each group tomorrow.
The organisers
Tomorrow we have the midterm webinar. All groups will be asked to
update their slides.
Every group should also think about their mini-publication! Remember
a mini-publication consists of the following sections
1. Description of problem
2. Description of state-of-the-art
3. Results of work during BioHackathon
4. Future work
This can simply be done in a Markdown document hosted on git. An example
can be found here
https://raw.githubusercontent.com/biohackrxiv/bhxiv-gen-pdf/master/example/logic/paper.md
which will be converted into a PDF that looks like
https://github.com/biohackrxiv/bhxiv-gen-pdf/blob/master/example/logic/LogicProgramming.pdf
These PDFs will be published with a DOI on
https://biohackrxiv.org/. If you are interested: during the
BioHackathon we are working on guidelines which can be found in the
BioHackrXiv channel on Slack.
We suggest to start reporting *today* by simply listing your
achievements and repositories in a Markdown document. You can add a
URL to that report on the group wiki today. If we find nothing we'll
approach each group tomorrow.
The organisers
LJ.Garcia
Apr 9, 2020, 7:39:47 AM4/9/20
to virtual biohackathon COVID-19 2020
Hi there,You are invited to a Zoom webinar.
When: Apr 9, 2020 01:00 PM London
Topic: Covid-19 Thursday webinarsPlease click the link below to join the webinar:
https://zoom.us/j/821064458?pwd=dStWNVd0cWU2MEZLMTc5RGpUVVR5UT09
Password: 974163Or iPhone one-tap :
US: +16465588656,,821064458# or +16699009128,,821064458#
Or Telephone:
Dial(for higher quality, dial a number based on your current location):
US: +1 646 558 8656 or +1 669 900 9128 or +1 253 215 8782 or +1 301 715 8592 or +1 312 626 6799 or +1 346 248 7799
Webinar ID: 821 064 458
International numbers available: https://zoom.us/u/adNN1JMAhe
When: Apr 9, 2020 01:00 PM London
Topic: Covid-19 Thursday webinarsPlease click the link below to join the webinar:
https://zoom.us/j/821064458?pwd=dStWNVd0cWU2MEZLMTc5RGpUVVR5UT09
Password: 974163Or iPhone one-tap :
US: +16465588656,,821064458# or +16699009128,,821064458#
Or Telephone:
Dial(for higher quality, dial a number based on your current location):
US: +1 646 558 8656 or +1 669 900 9128 or +1 253 215 8782 or +1 301 715 8592 or +1 312 626 6799 or +1 346 248 7799
Webinar ID: 821 064 458
International numbers available: https://zoom.us/u/adNN1JMAhe
Pjotr Prins
Apr 9, 2020, 7:44:45 AM4/9/20
to LJ.Garcia, virtual biohackathon COVID-19 2020
Dear all,
The first webinar is in 15 minutes by Michael Crusoe, an introduction
to the Common Workflow Language (CWL). If you are interested in
workflows/pipelines do attend! We are building our biohackathon public
sequence uploader on CWL and even if your are into WDL or Nextflow it
may pay to look at other approaches.
The second webinar is right after (scheduled in 1 hour and 15 minutes)
is Peter Amstutz on Arvados, a cloud service for bioinformatics HPC in
the cloud. The prototype version of the Biohackathon sequence uploader
is being deployed on Arvados. Peter will go into that.
The organisers.
On Thu, Apr 09, 2020 at 01:39:34PM +0200, LJ.Garcia wrote:
> Hi there,You are invited to a Zoom webinar.
> When: Apr 9, 2020 01:00 PM London
> Topic: Covid-19 Thursday webinarsPlease click the link below to join
> the webinar:
> [1]https://zoom.us/j/821064458?pwd=dStWNVd0cWU2MEZLMTc5RGpUVVR5UT09
> Password: 974163Or iPhone one-tap :
> US: [2]+16465588656,,821064458# or [3]+16699009128,,821064458#
> 8782 or [7]+1 301 715 8592 or [8]+1 312 626 6799 or [9]+1 346 248 7799
>
> --
> You received this message because you are subscribed to the Google
> Groups "virtual biohackathon COVID-19 2020" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to [11]virtual-biohacka...@googlegroups.com.
> To view this discussion on the web, visit
> [12]https://groups.google.com/d/msgid/virtual-biohackathon/CAPZUG%3DBQf
> -VXGS8LgdcsN0q_a5Cr2fwkJ%3DUTshNfjwuxO7w5zA%40mail.gmail.com.
>
> References
>
> 1. https://slack-redir.net/link?url=https://zoom.us/j/821064458?pwd=dStWNVd0cWU2MEZLMTc5RGpUVVR5UT09
> 2. tel:+16465588656,,821064458
> 3. tel:+16699009128,,821064458
> 4. tel:+16465588656
> 5. tel:+16699009128
> 6. tel:+12532158782
> 7. tel:+13017158592
> 8. tel:+13126266799
> 9. tel:+13462487799
> 10. https://slack-redir.net/link?url=https://zoom.us/u/adNN1JMAhe
> 11. mailto:virtual-biohacka...@googlegroups.com
> 12. https://groups.google.com/d/msgid/virtual-biohackathon/CAPZUG=BQf-VXGS8LgdcsN0q_a5Cr2fwkJ=UTshNfjw...@mail.gmail.com?utm_medium=email&utm_source=footer
The first webinar is in 15 minutes by Michael Crusoe, an introduction
to the Common Workflow Language (CWL). If you are interested in
workflows/pipelines do attend! We are building our biohackathon public
sequence uploader on CWL and even if your are into WDL or Nextflow it
may pay to look at other approaches.
The second webinar is right after (scheduled in 1 hour and 15 minutes)
is Peter Amstutz on Arvados, a cloud service for bioinformatics HPC in
the cloud. The prototype version of the Biohackathon sequence uploader
is being deployed on Arvados. Peter will go into that.
The organisers.
On Thu, Apr 09, 2020 at 01:39:34PM +0200, LJ.Garcia wrote:
> Hi there,You are invited to a Zoom webinar.
> When: Apr 9, 2020 01:00 PM London
> Topic: Covid-19 Thursday webinarsPlease click the link below to join
> the webinar:
> Password: 974163Or iPhone one-tap :
> US: [2]+16465588656,,821064458# or [3]+16699009128,,821064458#
> Or Telephone:
> Dial(for higher quality, dial a number based on your current location):
> US: [4]+1 646 558 8656 or [5]+1 669 900 9128 or [6]+1 253 215
> Dial(for higher quality, dial a number based on your current location):
> 8782 or [7]+1 301 715 8592 or [8]+1 312 626 6799 or [9]+1 346 248 7799
> Webinar ID: 821 064 458
> International numbers available: [10]https://zoom.us/u/adNN1JMAhe
>
> --
> You received this message because you are subscribed to the Google
> Groups "virtual biohackathon COVID-19 2020" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to [11]virtual-biohacka...@googlegroups.com.
> To view this discussion on the web, visit
> [12]https://groups.google.com/d/msgid/virtual-biohackathon/CAPZUG%3DBQf
> -VXGS8LgdcsN0q_a5Cr2fwkJ%3DUTshNfjwuxO7w5zA%40mail.gmail.com.
>
> References
>
> 1. https://slack-redir.net/link?url=https://zoom.us/j/821064458?pwd=dStWNVd0cWU2MEZLMTc5RGpUVVR5UT09
> 2. tel:+16465588656,,821064458
> 3. tel:+16699009128,,821064458
> 4. tel:+16465588656
> 5. tel:+16699009128
> 6. tel:+12532158782
> 7. tel:+13017158592
> 8. tel:+13126266799
> 9. tel:+13462487799
> 10. https://slack-redir.net/link?url=https://zoom.us/u/adNN1JMAhe
> 11. mailto:virtual-biohacka...@googlegroups.com
> 12. https://groups.google.com/d/msgid/virtual-biohackathon/CAPZUG=BQf-VXGS8LgdcsN0q_a5Cr2fwkJ=UTshNfjw...@mail.gmail.com?utm_medium=email&utm_source=footer
Pjotr Prins
Apr 9, 2020, 12:24:20 PM4/9/20
to Pjotr Prins, LJ.Garcia, virtual biohackathon COVID-19 2020
Michael Crusoe presented a great webinar on CWL and why we need it
today. You can view the early release of the video here:
http://ipfs.genenetwork.org/ipfs/QmSWparv88WM5ddawVaMRCtmyz8kJZTPd96ioUcepi55uf
Peter's webinar was postponed to tomorrow, we'll send a Zoom invite
soon.
today. You can view the early release of the video here:
http://ipfs.genenetwork.org/ipfs/QmSWparv88WM5ddawVaMRCtmyz8kJZTPd96ioUcepi55uf
Peter's webinar was postponed to tomorrow, we'll send a Zoom invite
soon.
Pjotr Prins
Apr 9, 2020, 7:13:07 PM4/9/20
to Pjotr Prins, LJ.Garcia, virtual biohackathon COVID-19 2020
Friday there will be a webinar by Peter Amstutz on the work we are
doing on the public sequence uploader and how Arvados and CWL are
underpinning that.
Time will be Friday 1300hrs UTC (2pm UK). Zoom invite to follow.
doing on the public sequence uploader and how Arvados and CWL are
underpinning that.
Time will be Friday 1300hrs UTC (2pm UK). Zoom invite to follow.
LJ.Garcia
Apr 10, 2020, 4:06:33 AM4/10/20
to Pjotr Prins, virtual biohackathon COVID-19 2020
Hello,
Please click on the link below to join the webinar:
https://zoom.us/j/834963587?pwd=VXZXNkRrSEh0UW9FdktlMEFYWGU0dz09
Password: 296045
Or with a tap of a finger on the iPhone :
United States of America: +13017158592,,834963587#,,#,296045# or +13126266799,,834963587#,,#,296045#
Or Telefon：
Wählen：
United States of America: +1 301 715 8592 or +1 312 626 6799 or +1 346 248 7799 or +1 646 558 8656 or +1 669 900 9128 or +1 253 215 8782
Webinar ID: 834 963 587
Password: 296045
Available international numbers: https://zoom.us/u/acKT3v4cuw
You are invited to a Zoom Webinar.
Subject: Arvados - Covid-19 Virtual BioHackathon webinar
When: 10.Apr.2020 15:00 Amsterdam, Berlin, Rome, Stockholm, Vienna
(6:00am PDT, 7:00am MDT, 8:00am CDT, 9:00am EDT, 10:00am BT, 1:00pm GMT, 2:00pm BST, 3:00pm CEST, 4:00pm EEST, 6:00pm PST, 6:30pm IST, 8:00pm IT, 9:00pm CST, 10:00pm JST, 11:00pm AEST, Sat 04-11 1:00am NZST)
Please click on the link below to join the webinar:
https://zoom.us/j/834963587?pwd=VXZXNkRrSEh0UW9FdktlMEFYWGU0dz09
Password: 296045
Or with a tap of a finger on the iPhone :
United States of America: +13017158592,,834963587#,,#,296045# or +13126266799,,834963587#,,#,296045#
Or Telefon：
Wählen：
United States of America: +1 301 715 8592 or +1 312 626 6799 or +1 346 248 7799 or +1 646 558 8656 or +1 669 900 9128 or +1 253 215 8782
Webinar ID: 834 963 587
Password: 296045
Available international numbers: https://zoom.us/u/acKT3v4cuw
Pjotr Prins
Apr 10, 2020, 8:34:54 AM4/10/20
to Pjotr Prins, LJ.Garcia, virtual biohackathon COVID-19 2020
Just a reminder: we have a webinar by @Peter Amstutz in half an hour.
Peter and others have been doing great work on creating
#public_sequence_resource. Peter Amstutz wil introduce Arvados, a
Hello,You are invited to a Zoom Webinar.
When: 10.Apr.2020 15:00 Amsterdam, Berlin, Rome, Stockholm, Vienna (6:00am PDT, 7:00am MDT, 8:00am CDT, 9:00am EDT, 10:00am BT, 1:00pm GMT, 2:00pm BST, 3:00pm CEST, 4:00pm EEST, 6:00pm PST, 6:30pm IST, 8:00pm IT, 9:00pm CST, 10:00pm JST, 11:00pm AEST, Sat 04-11 1:00am NZST)
https://zoom.us/j/834963587?pwd=VXZXNkRrSEh0UW9FdktlMEFYWGU0dz09
Peter and others have been doing great work on creating
#public_sequence_resource. Peter Amstutz wil introduce Arvados, a
cloud service for bioinformatics HPC in the cloud. The prototype
version of the Biohackathon sequence uploader is being deployed on
Arvados. Peter will go into that.
Webinar details for today:
version of the Biohackathon sequence uploader is being deployed on
Arvados. Peter will go into that.
Hello,You are invited to a Zoom Webinar.
When: 10.Apr.2020 15:00 Amsterdam, Berlin, Rome, Stockholm, Vienna (6:00am PDT, 7:00am MDT, 8:00am CDT, 9:00am EDT, 10:00am BT, 1:00pm GMT, 2:00pm BST, 3:00pm CEST, 4:00pm EEST, 6:00pm PST, 6:30pm IST, 8:00pm IT, 9:00pm CST, 10:00pm JST, 11:00pm AEST, Sat 04-11 1:00am NZST)
On Thu, Apr 09, 2020 at 11:24:18AM -0500, Pjotr Prins wrote:
LJ.Garcia
Apr 10, 2020, 12:26:27 PM4/10/20
to Pjotr Prins, virtual biohackathon COVID-19 2020
Hi there,You are invited to a Zoom webinar.
Topic: Covid-19 BH wrap up webinar
When: Apr 11, 2020 01:00 PM London
(5:00am PDT, 6:00am MDT, 7:00am CDT, 8:00am EDT, 9:00am BT, 12:00pm GMT, 1:00pm BST, 2:00pm CEST, 3:00pm EEST, 5:00pm PST, 5:30pm IST, 7:00pm IT, 8:00pm CST, 9:00pm JST, 10:00pm AEST, Sat 04-11 12:00am NZST)
Please click the link below to join the webinar:
https://zoom.us/j/657791489?pwd=OVNWemRVRkU3T25rMFFObktJV3F6UT09
Password: 941156Or iPhone one-tap :
US: +13017158592,,657791489# or +13126266799,,657791489#
Password: 941156Or iPhone one-tap :
US: +13017158592,,657791489# or +13126266799,,657791489#
Or Telephone:
Dial(for higher quality, dial a number based on your current location):
US: +1 301 715 8592 or +1 312 626 6799 or +1 346 248 7799 or +1 646 558 8656 or +1 669 900 9128 or +1 253 215 8782
Webinar ID: 657 791 489
Webinar ID: 657 791 489
Pjotr Prins
Apr 11, 2020, 7:50:50 AM4/11/20
to virtual biohackathon COVID-19 2020
After an amazing week of hacking non-stop, we are getting ready for our wrap-up session tomorrow
https://zoom.us/j/657791489?pwd=OVNWemRVRkU3T25rMFFObktJV3F6UT09
Password: 941156
You are invited to a Zoom webinar.
When: Apr 11, 2020 01:00 PM London
Topic: Covid-19 BH wrap up webinarPlease click the link below to join the webinar:
https://zoom.us/j/657791489?pwd=OVNWemRVRkU3T25rMFFObktJV3F6UT09
Password: 941156
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